What is a Population Bottleneck?

water being emptied from a blue glass bottleGenetic genealogists often hear the term population bottleneck referenced in various academic papers – but just what is that?  And why do we care?

A population bottleneck occurs when there is a dramatic reduction in the population of a particular group of people.  Think about the eruption of a volcano – Mt. Toba for example.

Human history is full of population reducing examples, some we know about, like the plague, but most we don’t.  And obviously, if the bottleneck was so severe that no one survived – then there are no descendants of those people today – and that’s an extinction event, not a bottleneck.  The only way we would ever know those people existed is if we found their remains and sequenced them today – like the Neanderthal and Denisovan skeletons.

As a point of clarity – the Neanderthal and Denisovan did survive – not as pure Neanderthals or Denisovans – but admixed into the homo sapiens population – and they are indeed, us.  If you have either European or Asian ancestry, then you have Neanderthal and Denisovan ancestry too.

How could that be – all of Europe and Asia descended from these Archaic people?  Probably the after-effects of a population bottleneck where a small group of people went on to become a large group of people.

Let’s look at an example.

The best example I can think of is the migration of the Asian people into the Americas.  These first people would populate all of North and South America and would become the indigenous people of these continents – by whatever name is applied today.  First People, Native Americans, American Indians – they are all of the same stock and the result of at least one population bottleneck.

That first bottleneck occurred when some people crossed over the land bridge, Beringia, between Asia and what is now Alaska.

beringia map

Erika Tamm et al – Tamm E, Kivisild T, Reidla M, Metspalu M, Smith DG, et al. (2007) Beringian Standstill and Spread of Native American Founders. PLoS ONE 2(9): e829. doi:10.1371/journal.pone.0000829. Also available from PubMed Central.

The bottleneck event that occurred there was that there weren’t very many people. It was probably a small group.  Possibly very small.  What do we know about them?

There were obviously males and females.

Assuming for purposes of discussion that all of the people who founded the Native American population came at once, or in what is referred to as one wave, we know that there were at least two men and 5 women.

How do we know that?  Because today we have Y haplogroups Q and C in the Native population and mitochondrial haplogroups A, B, C, D and X in that population as well.  Since the Y chromosome is passed from father to son unadmixed with any DNA from the mother, the haplogroups we see today are directly descended from those original founders.  Mitochondrial DNA is passed from the mother to all of her children, but only the females pass it on, so we get a direct pipeline view back to the founding mothers.

There may have been more individuals and haplogroups that arrived.  Some may have died out in Beringia or afterwards in subsequent bottleneck events.

Let’s say the group stayed together for a while.  Then, it got too big to support itself comfortably on the resources available.  In other words, the population began depleting the available resources.  So, the group separated by a few miles so that they could draw off of a different landscape where food was more abundant.

One group went 20 miles east and one group went 20 miles south.  It wasn’t meant to be permanent, but eventually, the split became permanent as that scenario repeated itself over time.

Eventually, one of the groups moved further south and small groups broke off from time to time and moved east across what would be the US and Canada.  Part of the group continued south along the Pacific and would populate Mexico, Central and South America.

Let’s say that one of those small bands of people that headed east wound up living in Montana, 12,500 years ago.  A child died, and they buried that child.

The group they separated from continued south and their descendants are found throughout Mexico, Central and South American today.

That child’s name is Anzick.  His skeleton was found in 1968 and his full genome was sequenced before he was reburied in 2013.  When his DNA was sequenced, we discovered, much to our amazement, that Anzick indeed matched people, primarily people from south of the US, at a level that could be interpreted to be contemporary.  How could that possibly be?

Think about a bottleneck in this fashion.

There are 4 people, 2 couples.  Each person’s DNA is represented by a color.  The two males are blue and green and the 2 females are pink and yellow, like on the left side of the pedigree chart shown below.

perez autosomal

In the first generation, they pass their DNA to their children and the children are blue/yellow and green/pink.  In the second generation, the children intermarry with the other couple’s children – because there are no choices.  All of the grandchildren of the original couple have DNA that is blue, yellow, green and pink.  The children and grandchildren don’t all carry the same segments of blue, yellow, green and pink – but all of them carry some part of the original 4 founders.  There is no orange or turquoise or red DNA to be found, so forever, until new people enter the landscape, they will pass the same segments of blue, green, yellow and pink DNA to their descendants.  In an isolated environment, they might not meet new humans for thousands of years – lets’ say 10,000 years.

So, if the Anzick child had blue, yellow, green and pink DNA and the contemporary Native people living in South America have blue, yellow, green and pink Native DNA from those same four founding ancestors, it stands to reason that they are going to match – because it’s the exact same DNA that has been passed around and around for thousands of years.

This matching is the effect of a population bottleneck.

We can think of other bottleneck events too.  For example, the Acadians were a bottleneck event.  A few shiploads of French Catholic people on an Island in the early 1600s – they didn’t have a lot of choice in terms of spouses. The genealogy saying is that if you’re related to one Acadian, you’re related to all Acadians, and it’s pretty much true.  Same with the Pilgrims and the individuals who came over on the Mayflower.

Some bottlenecks are religiously induced – Amish, Mennonite and Jewish, for example.  These people marry only within their religion.  Today, that’s called endogamy – but it’s a form of a bottleneck event.

We see the results of bottleneck events today in three ways in our DNA.  In both Y and mitochondrial DNA, we often see specific haplogroups or subgroups associated with specific populations – like Q and C in Native American Y DNA and subsets of A, B, C, D, X and possibly M in Native American mitochondrial DNA.

We also see the effects of bottleneck events in autosomal DNA.  We talk about segments that are IBD, identical by descent, and IBS, identical by state.  Identical by descent typically means we can attribute the DNA segment to a specific ancestor via triangulation.  Often, everything we can’t identify gets tossed into the IBS box, but it really shouldn’t.

When you hear people talk about IBS, or autosomal DNA segments that are identical by state, there are really two possibilities.  One is that the DNA is identical by chance.

The other option is that the DNA is identical by population.  This means that the DNA does indeed match because it came from a common ancestor – but that ancestor is beyond the genealogical timeframe.  That doesn’t mean the information isn’t useful.  Indeed, I think it’s very useful.  I want to know if a segment of my DNA is Native, even if I share that segment with lots of other Native people.  In fact, that’s exactly HOW we determine a specific autosomal segment is affiliated with Native or any other population group of people.  Certain segments are found in a higher percentage across the entire population group.  So, to throw these out in personal genetic genealogy by phasing which removes population based matches is a case of throwing the baby out with the bathwater.  I have several matches on my spreadsheet where I have the notation “Mennonite” or “Acadian” for example, because while I can’t sort out which specific ancestor the DNA came from, it assuredly came from the Acadian population based on the matches – and that’s very useful information.

Population bottlenecks may seem like a scientific term referencing something that happened long ago, but the effects of bottlenecks can be found in every one of us, beginning with Neanderthal and Denisovan DNA and probably including ancestors who survived, or willingly embraced beliefs which in essence created historical bottlenecks.



I receive a small contribution when you click on some of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

Thank you so much.

DNA Purchases and Free Transfers

Genealogy Services

Genealogy Research

15 thoughts on “What is a Population Bottleneck?

  1. I am an Acadian who lives in Nova Scotia, Canada. I am also grand-child (many generations later) of Jasmine. I find your information intriguing. I see that you have used the Acadians a s en example of a “bottleneck” example. I read your Jasmine Journey (which is how I decided to follow your entries).

    • I have been trying to decide whether to try a trip to Acadia this August or wait a year. I really want to go back but I don’t feel prepared enough yet with the genealogy. I’m thinking next year. I can hardly wait though. It will be something to look forward to.

  2. I do a demonstration similar to the diagram for my biology students. I place the same number of 6 different colors of small marbles into a long-stemmed wine bottle. This represents the different varieties of a particular gene in the pre-bottleneck population (the gene pool). Students then tilt the bottle and collect 6 marbles one at a time. Only rarely would they get equal mix of all of the colors.

  3. Very interesting post! I’ve been watching the “First Peoples” series on PBS and finding them fascinating, in light of what we learn here and what science has revealed in the last few years.

    I’ve come on an interesting situation I’ve not experienced before and would like your feedback, even if it’s just on what to make of a short segment which is heavily packed with SNPS.

    Five people who match me on FTDNA, each have 1) a short segment on chr 6 only 1.2 – 2.0 cm, each of which contain from 6000-7500 SNPs, and on chr 8 a short 2 cm segment that is perfectly aligned. They form a straight line. (On the chr browser it looks like a wee piece of coloured string). I tried duplicating this with numerous other matches and couldn’t and wonder tentatively if it might be a deep marker for our Native heritage? Both the original match I am working with and I share the same tribal background. His is current, he is over 50% genetically NA and knows his tribe. I haven’t contacted the others yet.

    • Start contacting people. Otherwise, you’re guessing:) The answers will be VERY interesting. Don’t forget that at GedMatch you can see your matches compared with another individual and painted with the ethnicity of specific segments. I’d try that.

      • I’ve been using Gedmatch for a while now but I don’t recall seeing anything about painting segments with ethnicity. Can you provide a pointer to that facility?

          • Thanks, Roberta but there are an awful lot of options to choose from and I have no idea which to use. Can you make any recommendations for someone who is 90% Jewish Diaspora?

          • You’ll need to do some experimentation. I use this when I’m trying to determine if someone matches me on a Native segment, which is a small part of my genome. How you use the tool depends on your goals and what you are trying to achieve.

  4. Whew ! That takes a load off. It explains somewhat why in the 14 matches I have in Family finder FTDNA that I am double matched with 11 or 12 on both Y and Mt. There for a while I was getting worried that we were all products of generational habitual inbreeding of some cultish level ! just kidding, but I found it odd. The last ice age made strange bedfellows, or at least they kept warm across Eurasia.

  5. I realized recently how loosely that term is used, and is used in conjunction with Founder’s population/effect.

    While working on the Pitcairn family genealogies the past several weeks, I saw how they went through a bottleneck. Staring with the year 1790 through 1856 –> 1859 –> 1936 –> 1996 –> 2014 the population went from 27 –> 193 –> 16 –> 250 –> 43 –> 56. So it grew, reduced drastically, grew, reduced & slowly recovered but that they predict will end soon.

    On the island of Molokai where I come from, they estimated less than 2,000 in 1778, and in the 1950s they said it was around 10,000 and I remember several years ago it was 6,700 and now they say it’s almost at 8,000. In Hawaii from 1778 –> 1872 –> 1900 –> 2000 the population for Native Hawaiians was 300,000 – 800,000 (estimated) –> 51,431 –> 37,635 –> 460,000.

    In those two examples we know what happens. I get matches with Maori people of New Zealand or Samoans, Tongans, all of whom we shared common ancestors from at least 800 years ago. Or getting a match with a man from Norfolk island whose ancestors left Pitcairn island in 1856 & married other outsiders coming to that island, or with a man whose mother is from Rotuma island (Fiji) a place where 3,5000 years ago our common ancestors settled that area. This man’s ancestors stayed in that area whereas mine eventually ended up in Hawaii thousands of years after.

    It may have started from a long time ago, but with recent bottle necking, it seems to really affect all of us and we can see it with autosomal results.

  6. Thank you for providing such a clear explanation. I am part of the AJ endogamous population and totally frustrated by having so many matches and yet no clue how we are related, even going back four generations. This post helped me understand why.

  7. Roberta, some of your folks are from the deep south. Makes me wonder if there was a society-wide bottleneck here after the American Civil War?

  8. Pingback: DNAeXplain Archives – Basic Education Articles | DNAeXplained – Genetic Genealogy

Leave a Reply